Molecular Dynamics Study On Structure And Binding Energy Of Coagulation Factor Xa Containing Water Molecules

The coagulation factor Xa(short for FXa)is a key enzyme in the process of blood coagulation.It is also an important target for antithrombotic drugs.In recent years,water molecules in the biological molecules are taken more attention in the simulation.These water molecules affect the structures and functions of proteins.In this work,the molecular dynamics simulation is preformed to study the effects on the structure and binding energy for the FXa complexes with and without water molecules.Compared the FXa complexes containing no water molecules with those containing water molecules,hydrogen bonds among the water molecules,residues,and ligand make the structures of the FXa complex more stable.The binding energy results show that the correlation between the MM-GB/SA calculation and experimental data has an improvement by taking the water molecule into consideration in the FXa.All the results show that the water molecules have an influence on the FXa complexes.Therefore,in the simulation,the water molecules should be as a part of FXa.